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TET2 is a close relative of TET1, an enzyme that converts 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) in DNA. The gene encoding TET2 resides at chromosome 4q24, in a region showing recurrent microdeletions and copy-neutral loss of heterozygosity (CN-LOH) in patients with diverse myeloid malignancies. Somatic TET2 mutations are frequently(More)
The increasing volume of ChIP-chip and ChIP-seq data being generated creates a challenge for standard, integrative and reproducible bioinformatics data analysis platforms. We developed a web-based application called Cistrome, based on the Galaxy open source framework. In addition to the standard Galaxy functions, Cistrome has 29 ChIP-chip- and(More)
MOTIVATION Transcription factors (TFs) play a key role in gene regulation by binding to target sequences. In silico prediction of potential binding of a TF to a binding site is a well-studied problem in computational biology. The binding sites for one TF are represented by a position frequency matrix (PFM). The discovery of new PFMs requires the comparison(More)
Dioxygenases of the Ten-Eleven Translocation (TET) family are 5-methylcytosine oxidases that convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) and further oxidation products in DNA. We show that Tet1 and Tet2 have distinct roles in regulating 5hmC in mouse embryonic stem cells (mESC). Tet1 depletion diminishes 5hmC levels at transcription(More)
5-hydroxymethylcytosine (5hmC) is a modified base present at low levels in diverse cell types in mammals. 5hmC is generated by the TET family of Fe(II) and 2-oxoglutarate-dependent enzymes through oxidation of 5-methylcytosine (5mC). 5hmC and TET proteins have been implicated in stem cell biology and cancer, but information on the genome-wide distribution(More)
OBJECTIVE To examine the effect of systolic and diastolic blood pressure achieved in the first year of treatment on all cause mortality in patients newly diagnosed with type 2 diabetes, with and without established cardiovascular disease. DESIGN Retrospective cohort study. SETTING United Kingdom General Practice Research Database, between 1990 and 2005.(More)
Transcription factors play a key role in gene regulation by interacting with specific binding sites or motifs. Therefore, enrichment of binding motifs is important for genome annotation and efficient computation of the statistical significance, the p-value, of the enrichment of motifs is crucial. We propose an efficient approximation to compute the(More)
BACKGROUND The objective of this review was to assess the uptake of WHO recommended integrated perinatal prevention of mother-to-child transmission (PMTCT) of HIV interventions in low- and middle-income countries. METHODS AND FINDINGS We searched 21 databases for observational studies presenting uptake of integrated PMTCT programs in low- and(More)
BACKGROUND The UK introduced an ambitious national strategy to reduce population levels of salt intake in 2003. The aim of this study was to evaluate the impact of this strategy on salt intake in England, including potential effects on health inequalities. METHODS Secondary analysis of data from the Health Survey for England. Our main outcome measure was(More)
BACKGROUND Patients are increasingly rating their family physicians on the Internet in the same way as they might rate a hotel on TripAdvisor or a seller on eBay, despite physicians' concerns about this process. OBJECTIVE This study aims to examine the usage of NHS Choices, a government website that encourages patients to rate the quality of family(More)